This is an automatically-produced report from shinyQC. The analyzed data
contains 630 features and 88 samples.
Use the settings
Categorical variable = name.The mosaic plot was not called within the shiny application. Use default settings.
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Categorical variable 1 = name andCategorical variable 2 = name.The ‘Histogram Features’ plot was not called within the shiny application. Use default settings.
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Binwidth = 1.
The ‘Histogram Features along variable’ plot was not called within the shiny application. Use default settings.
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Variable for stratification = name andBinwidth = 1.The ‘Upset’ plot was not called within the shiny application. Use default settings.
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Variable for stratification = name.The ‘Histogram Features’ plot was not called within the shiny application. Use default settings.
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Binwidth = 1.
The ‘Histogram Features along variable’ plot was not called within the shiny application. Use default settings.
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Variable for stratification = name andBinwidth = 1.The ‘Upset’ plot was not called within the shiny application. Use default settings.
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Variable for stratification = name.Use the settings
Display log2 values? = FALSE andType of display = FALSE.Use the settings
Select variable = ,Select level to highlight = ,Select data input = raw,Select aggregation = sum,Select smoothing method = loess, andSelect variable to order samples = .The ‘MA plot’ was not called within the shiny application. Use default settings.
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group = all,plot = all,Data set for the MA plot = raw, andlines = FALSE.The ‘ECDF’ plot was not called within the shiny application. Use default settings.
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Data set for the ECDF plot = raw,Sample = 1_Plasma_4C_0_C1, andgroup = all.The ‘Distance matrix’ plots were not called within the shiny application. Use default settings.
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annotation = name anddistance method = euclidean.The ‘PCA’ plot was not called within the shiny application. Use default settings.
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x-axis = PC1,y-axis = PC2,scale = TRUE,center = TRUE, andHighlight = none.The ‘PCoA’ plot was not called within the shiny application. Use default settings.
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x-axis = Axis.1,y-axis = Axis.2,Distance measure = euclidean, andHighlight = none.The ‘NMDS’ plot was not called within the shiny application. Use default settings.
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x-axis = MDS1,y-axis = MDS2,Distance measure = euclidean, andHighlight = none.## Run 0 stress 9.8761e-05
## Run 1 stress 9.754276e-05
## ... New best solution
## ... Procrustes: rmse 2.886935e-05 max resid 0.0001422001
## ... Similar to previous best
## Run 2 stress 9.86572e-05
## ... Procrustes: rmse 1.153469e-05 max resid 3.100026e-05
## ... Similar to previous best
## Run 3 stress 9.594461e-05
## ... New best solution
## ... Procrustes: rmse 0.0001095138 max resid 0.0003442642
## ... Similar to previous best
## Run 4 stress 9.597091e-05
## ... Procrustes: rmse 5.576928e-05 max resid 0.0003360568
## ... Similar to previous best
## Run 5 stress 9.972704e-05
## ... Procrustes: rmse 0.0001139659 max resid 0.0003331439
## ... Similar to previous best
## Run 6 stress 0.0001031675
## ... Procrustes: rmse 0.0001307271 max resid 0.0003813627
## ... Similar to previous best
## Run 7 stress 9.736016e-05
## ... Procrustes: rmse 0.0001224382 max resid 0.0003583916
## ... Similar to previous best
## Run 8 stress 9.986547e-05
## ... Procrustes: rmse 0.0001047054 max resid 0.0003592288
## ... Similar to previous best
## Run 9 stress 9.13122e-05
## ... New best solution
## ... Procrustes: rmse 6.509991e-05 max resid 0.0002655749
## ... Similar to previous best
## Run 10 stress 9.823867e-05
## ... Procrustes: rmse 0.0001081686 max resid 0.000279633
## ... Similar to previous best
## Run 11 stress 9.778621e-05
## ... Procrustes: rmse 6.981572e-05 max resid 0.000270329
## ... Similar to previous best
## Run 12 stress 9.798048e-05
## ... Procrustes: rmse 0.0001144515 max resid 0.0004243048
## ... Similar to previous best
## Run 13 stress 9.98246e-05
## ... Procrustes: rmse 8.444349e-05 max resid 0.0004618941
## ... Similar to previous best
## Run 14 stress 9.955774e-05
## ... Procrustes: rmse 0.0001026056 max resid 0.0004400828
## ... Similar to previous best
## Run 15 stress 9.889913e-05
## ... Procrustes: rmse 7.846163e-05 max resid 0.000279398
## ... Similar to previous best
## Run 16 stress 9.731138e-05
## ... Procrustes: rmse 8.529584e-05 max resid 0.0002259614
## ... Similar to previous best
## Run 17 stress 9.410327e-05
## ... Procrustes: rmse 6.725978e-05 max resid 0.0002614167
## ... Similar to previous best
## Run 18 stress 9.432414e-05
## ... Procrustes: rmse 7.68446e-05 max resid 0.000506901
## ... Similar to previous best
## Run 19 stress 9.893589e-05
## ... Procrustes: rmse 8.42744e-05 max resid 0.0002169461
## ... Similar to previous best
## Run 20 stress 9.898755e-05
## ... Procrustes: rmse 8.362943e-05 max resid 0.000181727
## ... Similar to previous best
## *** Solution reached
The ‘tSNE’ plot was not called within the shiny application. Use default settings.
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x-axis = X1,y-axis = X2,Perplexity = 10,Number of iterations = 1000,Number of retained dimensions in intial PCA = 10,Output dimensionality = 3, scale = TRUE,center = TRUE, andHighlight = none.The ‘UMAP’ plot was not called within the shiny application. Use default settings.
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x-axis = X1,y-axis = X2,Minimum distance = 0.1,Number of neighbors = 15,Spread = 1, andHighlight = none.